rs12915116

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

TTBK2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0134 (4018/29980,GnomAD)
T=0094 (2736/29118,TOPMED)
T=0084 (423/5008,1000G)
T=0181 (697/3854,ALSPAC)
T=0181 (670/3708,TWINSUK)

Position: chr15:42782482 (GRCh38.p7) (15q15.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 64 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 15	NC_000015.10:g.42782482C>T
GRCh37.p13 chr 15	NC_000015.9:g.43074680C>T
TTBK2 RefSeqGene	NG_012664.1:g.143328G>A

Gene: TTBK2, tau tubulin kinase 2(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TTBK2 transcript	NM_173500.3:c.	N/A	Intron Variant
TTBK2 transcript variant X1	XM_005254171.4:c.	N/A	Intron Variant
TTBK2 transcript variant X4	XM_005254173.4:c.	N/A	Intron Variant
TTBK2 transcript variant X2	XM_006720402.3:c.	N/A	Intron Variant
TTBK2 transcript variant X3	XM_006720403.3:c.	N/A	Intron Variant
TTBK2 transcript variant X5	XM_017021950.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.992	T=0.008
1000Genomes	American	Sub	694	C=0.920	T=0.080
1000Genomes	East Asian	Sub	1008	C=0.997	T=0.003
1000Genomes	Europe	Sub	1006	C=0.834	T=0.166
1000Genomes	Global	Study-wide	5008	C=0.916	T=0.084
1000Genomes	South Asian	Sub	978	C=0.810	T=0.190
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.819	T=0.181
The Genome Aggregation Database	African	Sub	8732	C=0.970	T=0.030
The Genome Aggregation Database	American	Sub	838	C=0.910	T=0.090
The Genome Aggregation Database	East Asian	Sub	1622	C=0.999	T=0.001
The Genome Aggregation Database	Europe	Sub	18486	C=0.804	T=0.195
The Genome Aggregation Database	Global	Study-wide	29980	C=0.866	T=0.134
The Genome Aggregation Database	Other	Sub	302	C=0.790	T=0.210
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.906	T=0.094
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.819	T=0.181

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs12915116	0.000242	alcohol dependence	21314694

eQTL of rs12915116 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr15:43074680	CDAN1	ENSG00000140326.8	C>T	3.8238e-9	45356	Cerebellum

meQTL of rs12915116 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr15	43027062	43027228	E067	-47452
chr15	43027261	43027305	E067	-47375
chr15	43027358	43027506	E067	-47174
chr15	43027622	43027761	E067	-46919
chr15	43027805	43027893	E067	-46787
chr15	43066075	43066198	E067	-8482
chr15	43066225	43066284	E067	-8396
chr15	43027622	43027761	E068	-46919
chr15	43027805	43027893	E068	-46787
chr15	43065833	43065873	E068	-8807
chr15	43066075	43066198	E068	-8482
chr15	43066225	43066284	E068	-8396
chr15	43027805	43027893	E069	-46787
chr15	43064437	43064698	E069	-9982
chr15	43064762	43064829	E069	-9851
chr15	43027062	43027228	E070	-47452
chr15	43027261	43027305	E070	-47375
chr15	43027358	43027506	E070	-47174
chr15	43027622	43027761	E070	-46919
chr15	43027622	43027761	E071	-46919
chr15	43027805	43027893	E071	-46787
chr15	43030134	43030322	E071	-44358
chr15	43064014	43064077	E071	-10603
chr15	43064437	43064698	E071	-9982
chr15	43066225	43066284	E071	-8396
chr15	43064437	43064698	E072	-9982
chr15	43066075	43066198	E072	-8482
chr15	43066225	43066284	E072	-8396
chr15	43026168	43026229	E073	-48451
chr15	43026360	43026480	E073	-48200
chr15	43026534	43026638	E073	-48042
chr15	43026640	43026696	E073	-47984
chr15	43026703	43026761	E073	-47919
chr15	43027009	43027059	E073	-47621
chr15	43027062	43027228	E073	-47452
chr15	43027261	43027305	E073	-47375
chr15	43027358	43027506	E073	-47174
chr15	43027622	43027761	E073	-46919
chr15	43027805	43027893	E073	-46787
chr15	43051168	43051387	E073	-23293
chr15	43051411	43051630	E073	-23050
chr15	43062832	43063015	E073	-11665
chr15	43064014	43064077	E074	-10603
chr15	43064437	43064698	E074	-9982
chr15	43064762	43064829	E074	-9851
chr15	43027622	43027761	E081	-46919
chr15	43027805	43027893	E081	-46787
chr15	43062832	43063015	E081	-11665
chr15	43063051	43063176	E081	-11504
chr15	43063303	43063343	E081	-11337
chr15	43063545	43063639	E081	-11041
chr15	43063667	43063733	E081	-10947
chr15	43064014	43064077	E081	-10603
chr15	43064437	43064698	E081	-9982
chr15	43065833	43065873	E081	-8807
chr15	43066075	43066198	E081	-8482
chr15	43066225	43066284	E081	-8396
chr15	43075389	43075445	E081	709
chr15	43075511	43075565	E081	831
chr15	43076996	43077163	E081	2316
chr15	43077215	43077255	E081	2535
chr15	43027622	43027761	E082	-46919
chr15	43027805	43027893	E082	-46787
chr15	43064014	43064077	E082	-10603

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr15	43028351	43030099	E067	-44581
chr15	43028351	43030099	E068	-44581
chr15	43028351	43030099	E069	-44581
chr15	43028351	43030099	E070	-44581
chr15	43028351	43030099	E071	-44581
chr15	43028351	43030099	E072	-44581
chr15	43028351	43030099	E073	-44581
chr15	43028351	43030099	E074	-44581
chr15	43028351	43030099	E081	-44581
chr15	43028351	43030099	E082	-44581